The new commander of the Egyptian military, while a student at the U.S. Army War College seven years ago, wrote a lengthy paper in which he called for the U.S. to withdraw its military forces from the Middle East, encouraged it to revamp the way it provides aid to Egypt in order to foster economic development and criticized the U.S. as pursuing a “one-sided” policy in the region in which concern about Israeli security trumped all other interests.

Lt. Gen. Sedky Sobhy’s 10,630-word treatise, essentially a thesis for the master of strategic studies degree he earned from the college in 2005, provides an unusually candid and detailed look into the thinking of the No. 2 official in Egypt’s new military hierarchy, which was set in place Sunday in a surprise series of moves by Egypt’s first elected president, Mohammed Morsi.

Then a brigadier general, Sobhy titled the piece “The U.S. Military Presence in the Middle East Issue and Prospects.” In many ways it reflects the thinking of the nearly 500,000 soldiers and 1 million reservists he now commands.

He wrote that the United States “erroneously” defines its Middle East policy around Israel, which he said conducted “illegitimate and internationally condemned occupation” of Arab territories. “Nothing defines better the ideological struggle that the United States has to overcome in the Middle East than the hostility and negative perceptions that exist in the region because of the (United States’) unique and one-sided relationship with Israel,” he wrote.

He also worried about the Bush administration’s promotion of democracy and whether it could lead to change that would harm American interests. “The present United States administration’s public pronouncements about the ‘march of democracy’ in the Middle East must be contrasted with the U.S. strategic interests regarding stability in the region,” Sobhy wrote, explaining later, “The process of democratization must be handled carefully so that in and of itself does not result in the undesirable state of political and social instability.”

That must include religious legitimacy, Sobhy said. He said U.S. officials didn’t fully appreciate how much Islam must be incorporated into a democratic system. “The Islamic religion is strongly interlinked to various degrees with the functioning of most Arab governments and their respective societies,” he said.

Sobhy was thrust into his new position Sunday when Morsi, an Islamist and former member of the Muslim Brotherhood, forced the defense minister, Field Marshal Mohammed Tantawi, and the No. 2 military official, Lt. Gen. Sami Anan, into retirement, a move that surprised many analysts and left them pondering what the ramifications would be. Morsi is the first Egyptian leader who hasn’t served in the military, and the first avowed Islamist to head the country’s government.

How his rule will change the way Egypt is governed and its relationship with the United States has been a focus of discussion since he was elected in June. Sobhy’s selection to head the armed forces may provide a window into some of the likely changes ahead.

For example, while Egypt under deposed President Hosni Mubarak had frosty relations with Iran, Sobhy called in his paper for direct U.S.-Iran communications, calling it a “realistic approach.”

Sobhy wrote the paper, known at the war college as a strategic research project, over a six-month period beginning in September 2004. At the time, U.S. troops were engaged in heavy fighting with insurgents in Iraq. Indeed, the second U.S. Marine Corps offensive in Fallujah occurred as he wrote the paper. According to his adviser on the project, that shaped his thinking.

Professor Douglas Lovelace, the director of the Army War College’s Strategic Studies Institute and Sobhy’s adviser, remembered him as a “bold thinker,” charming and a “very impressive officer” who often offered thoughts counter to the conventional thinking at the time.

“I do recall he was provocative and an original thinker,” Lovelace said. “It was not surprising that he would either fail completely or rise to the top.”

The existence of the document was first publicized by a blogger known as @Arabist, who highlighted it in a Twitter posting. A search of the Army War College Library catalog online found no other publications by Sobhy.

Thousands of top commanders from around the world have trained at U.S. war and command colleges, where midcareer officers often go to obtain additional academic training or graduate degrees. American officials open the colleges to other nations’ military commanders to encourage relationships as military leaders rise through the ranks as well as to expose them to U.S. military thinking. Egypt has been one of the biggest participants in the program, spurred by the 1979 Camp David peace accords. The colleges all have notable graduates.

Pakistan’s army chief of staff, Gen. Ashfaq Parvez Kayani, and former Rwandan President Paul Kagame, who ended the genocide there, studied at the U.S. Army Command and General Staff College at Fort Leavenworth, Kan. Egypt’s new defense minister, Abdel-Fattah el Sissi, like Sobhy attended the Army War College in 2006.

The Army War College, in Carlisle, Pa., has accepted 40 to 70 students a year for the 10-month program. Lovelace said each student’s work represented his own thinking, not that of the U.S. or home governments.